One of the great things about programming in Java is that it runs straight off in Linux and Windows without even the need to recompile. I've never had any of the problems that I've heard described elsewhere, but maybe I haven't covered the same kind of areas. However, I've written platform games, 3D shooters, desktop applications, database connections, and I think the only time when I've had to include a bit of code that says "if (linux) { do this } else { ... }" etc..., and that was because of slightly difference font sizes, which is fair enough (and probably for patent reasons).
This does sometimes lead you to a false sense of security though. I've been caught out several times by case-sensitivity. A program will work fine on Windows, but then I run it on Linux and it can't find the file "xyz.3ds" because the filename is actually called "Xyz.3ds". Still, a bit of testing should sort that out, and we all do that, don't we?
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